Antigen

Antigen Class

TFs and others

Antigen

Lmnb1

Cell type

Cell type Class

Liver

Cell type

Liver

MeSH Description

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Sample

source_name

Liver

tissue

liver

genotype

WT

age

4 months

diet

Western, 8 wks

chip antibody

Lamin B1

Sequenced DNA Library

library_name

GSM5916360

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

[RNA-Seq] Liver RNA was isolated from mice on control and Western diet (8 weeks and 12 weeks). Quality of RNA samples was analyzed using Agilent RNA 6000 Nano Kit (Bioanalyzer, Agilent Technologies). Samples with RIN scores above 9.5 were used in library preparation. 1 µg of total RNA was used to isolate mRNA (NebNext Poly(A) mRNA Magnetic Isolation Module). [RNA-Seq] Libraries of resulting mRNA were prepared using NebNext Ultra II RNA library preparation kit. All samples were sequenced on Illumina NextSeq 500. [ChIP-Seq] Snap-frozen liver (100 mg) from mice on normal and Western diet (8 weeks and 12 weeks) or from normal and NAFLD patients was used to prepare chromatin. Foxa2‐specific rabbit antiserum (Seven Hills Bioreagents, WRAB‐1,200) and rabbit antibody to lamin B1 (Abcam, Ab16048) were used for immunoprecipitation. [ChIP-Seq] Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Multiplex adapters were then ligated to the ends of the modified DNA. After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp insert plus ~130-bp adaptor and PCR primer sequences) were isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. All libraries were sequenced on Illumina NextSeq 500.

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

49106532

Reads aligned (%)

63.9

Duplicates removed (%)

23.0

Number of peaks

474 (qval < 1E-05)

mm9

Number of total reads

49106532

Reads aligned (%)

63.8

Duplicates removed (%)

23.1

Number of peaks

449 (qval < 1E-05)